Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
9 hits were found for GAGCAUUGACACAUGUGCA (2 guide strand hits and 7 sense strand hits.)
Hits to Guide strand
| Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
| NM_002526 | NT5E | 2645 | 2663 | G | A | G | C | A | U | U | u | A | C | A | C | A | U | G | U | u | a | A | 11 | 3 | 8 | c | false | <90% | 3547 | ||
| NM_152630 | FAM46D | 877 | 895 | a | A | G | C | A | a | U | G | A | C | A | C | A | U | u | U | G | C | A | 9 | 3 | 8 | c | false | <90% | 3027 | ||
Hits to Sense strand
| Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
| NM_000328 | RPGR | 404 | 422 | c | c | a | A | C | A | U | G | U | G | U | C | A | A | a | G | C | U | C | 42 | 4 | 11 | c | false | <90% | 3082 | ||
| NM_001034853 | RPGR | 404 | 422 | c | c | a | A | C | A | U | G | U | G | U | C | A | A | a | G | C | U | C | 42 | 4 | 11 | c | false | <90% | 4718 | ||
| NM_018046 | AGGF1 | 3490 | 3508 | g | G | C | A | C | A | g | G | U | G | U | C | A | c | U | G | C | U | C | 12 | 3 | 6 | c | false | <90% | 4480 | ||
| XM_940609 | FLJ25076 | 3707 | 3725 | c | G | C | A | C | A | U | G | U | G | c | C | A | A | U | a | C | U | C | 10 | 3 | 9 | c | false | <90% | 4305 | ||
| XM_059689 | FLJ25076 | 3821 | 3839 | c | G | C | A | C | A | U | G | U | G | c | C | A | A | U | a | C | U | C | 10 | 3 | 9 | c | false | <90% | 4419 | ||
| XM_045911 | STXBP5L | 3900 | 3918 | U | G | C | A | C | A | U | G | a | G | U | u | A | A | U | G | C | U | g | 1 | 3 | 8 | false | <90% | 5179 | |||
| XM_938898 | STXBP5L | 3900 | 3918 | U | G | C | A | C | A | U | G | a | G | U | u | A | A | U | G | C | U | g | 1 | 3 | 8 | false | <90% | 5179 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1709
View matched accessions
3 prime seed match details
Immunostimulatory motif search results
UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
Motif found in sense strand
GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).
Settings used for search
Scores were calculated using scoring scheme SS1
Using AVG scoring mode.
Hit scores
| Parameter | Spec. Score cut-off | Colour | Comment |
| Hit to same gene | Colour | Hits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit. | |
| High scoring hit | ≥80 | Colour | Hits are very likely to cause an off-target effect |
| Medium scoring hit | <80¸≥40 | Colour | Hits with a small chance of causing an off target effect. |
| Low scoring hit | Colour | Hits very unlikely to cause an off-target effect |
The mismatches are colour coded based on the weighting of that position.
| Cut-off | Colour |
| Match | Colour |
| Wobble base pairs (G-U) | Colour |
| Critical bases (none) | Colour |
| 0.6 bits | Colour |
| 0.4 bits | Colour |
| 0.2 bits | Colour |
SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).
Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer